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ARS Home » Southeast Area » Florence, South Carolina » Coastal Plain Soil, Water and Plant Conservation Research » Research » Publications at this Location » Publication #295021

Title: Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)

Author
item TYAGI, PRIYANKA - North Carolina State University
item GORE, MICHAEL - Cornell University - New York
item BOWMAN, DARYL - North Carolina State University
item Campbell, Benjamin - Todd
item UDALL, JOSHUA - Brigham Young University
item KURAPARTHY, VASU - North Carolina State University

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2013
Publication Date: 11/4/2013
Citation: Tyagi, P., Gore, M.A., Bowman, D.T., Campbell, B.T., Udall, J.A., Kuraparthy, V. 2014. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Journal of Theoretical and Applied Genetics. 127:283-295.

Interpretive Summary: Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. In this study, we genotyped a large set of cotton accessions representing more than 100 years of US upland cotton breeding with molecular markers in order to establish the genetic diversity and population structure in tetraploid cotton. Population structure analysis revealed identified five subgroups corresponding to Southeastern, Midsouth, Southwest and Western zones of cotton growing areas in United States. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. Core sets of accessions representing different levels of allelic richness were identified in Upland cotton. The establishment of core sets in this study set the stage for future genetic and genomic analyses aimed to better utilize existing genetic variation in upland cotton breeding programs.

Technical Abstract: Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 Gossypium barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty two percent of the alleles in Upland accessions were unique specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest and Western zones of cotton growing areas in United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information although there were a few exceptions. Furthermore, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity and population structure of the diversity panel and identification of core sets in this study may be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.